Here's a quick list of some hw2 ships and their good points/bad points, to help newcomers to the game. This is entirely personal opinion, and is mostly based on 1v1 games. This isn't a complete list of ship types, just the ones that I commonly build and have most experience with. I'll edit this to include vaygr once i've written one for them.
Collectors - obviously crucial, as they supply ru which really is your lifeblood. However, don't make the mistake of building too many near the start of the game, as this can allow your opponent to get too far ahead in offensive ships, and you'll quickly find yourself in a position you can't win from. Try to avoid putting too many collectors in any one patch. Upgrading the collectors to lvl1 armour can be surprisingly useful in some situations, although obviously you don't want to waste the cash on that unless you know they're going to get attacked. Upgrading to give them the repair abillity can be useful late on in a game.
Refineries - a useful drop off point for your collectors. Bear in mind though that your ms and carrier are also both perfectly good drop off points, so the cash may well be better spent on other ships early in the game - in some situations they're invaluable, but you can get through a lot of games without building one.
Probes - scouting the enemy is very important in this game, and I usually use probes to do so rather than scouts. How many you need obviously depends on the size of the map, and your opponent will obviously be trying to kill them (as you should be trying to kill theirs). A good situation is to have 1 at your ms, which you can dispatch quickly if you need to, but also helps prevent people sneaking around the flanks, and another one near your opponent's ms so you can see what they're doing. When you're sending probes to the enemy, try and position them so that the enemy ship you're spying on is near the edge of the probe's range, so that it's harder for them to spot the probe and kill it.
Scouts - personally i don't tend to use scouts, as they come out of your fighter allowance, and i'd rather use probes and have 14 intereceptors (or ints/bombers) in most games. They can be good for some quick scouting, and it's far easier to keep them alive than your probes. Imho, emp isn't worth bothering with for hiigaran, its cost outweighs its effectiveness in most situations. Note: as opposed to hw or hwc, scouts in hw2 are NOT effective combat craft. Even in large numbers, they won't kill anything larger than a probe. Their use is purely scouting/emp.
Interceptors - fantastically useful, and essential in most games. You really need to look after your interceptors - if you get yourself in a position where the enemy has far more sc than you, you're normally in serious trouble. Their main use is in killing other strike craft - use them to fight your opponent's ints/acs until they have killed them, and then if you have sufficient numbers you can start to look into killing collectors, although i tend more to holding them back and keeping them alive until later in the game. I don't want to go into fighter tactics in detail here, i'll save it for another thread. In sufficient numbers, they are also capable of taking out enemy corvettes, though you really do need to be sure of the numerical superiority. Speed upgrades for interceptors are extremely useful - lvl1 speed ints will wipe the floor with unupgraded ints, and lvl2 will beat lvl1 in a similar way. Bear in mind that when you're fighting a vaygr player, they can get to lvl2 speed far quicker with their acs, and also have a larger number of them - so try and keep your fighters back until you have the adv res module built and have researched lvl2 speed if you can.
Bombers - bombers are incredibly effective, but they really need to be used at the right time. If your opponent has 14 interceptors, and you try and use 10 ints/4 bombers, you will lose badly, as bombers will die against interceptors, and your smaller number of ints will lose very quickly. Bombers should only be brought into play if the opponent has decided not to go for so many fighters, or you have already killed all or most of his interceptors. If you do get the chance to build them they can be very effective at killing frigates (except flak/assault), picking off modules from the ms or a carrier, killing collectors, or actually killing a carrier.
Gun Corvettes - good ships, although they tend to come into play more against vaygr than against a hiigaran opponent. They do not slaughter fighters as quickly as you might imagine, but they are very durable (except against torpedo frigates, pulsar corvs or missile corvs, and to a certain extent lance fighters). Their main use is when playing against a vaygr opponent, to build them after you've maxed out your interceptors to counteract your opponent's superior fighter numbers quickly. All their upgrades are fairly worthwhile.
Pulsar Corvettes - good ships, but I don't tend to use them in most games simply because they don't fit into the pattern of my games. They are good at killing other corvettes, and in numbers can also kill collectors, carriers, destroyers and most frigates (except torps) fairly effectively. All their upgrades are fairly worthwhile.
Torpedo frigates - exceptionally effective, and I tend to use these in most the games I play, even though they've been toned down in the patch. They are a real multi-purpose frigate - they absolutely slaughter corvettes (although laser vettes also kill torps very quickly, so watch out for them and make sure to target them early). They can do relatively effective damage against fighters, although they will not kill them at any great pace, and will die against bombers. With the 'improved torpedo' upgrade they also kill other frigates, carriers and collectors very effectively. In sufficiently high numbers they can also kill destroyers, although even a single destroyer will punch quite a hole through your frigate force, so only commit against one if you're really sure of the numbers (personally i'd only really feel happy going in if I had 7+). The improved torpedo upgrade is crucial despite its cost, unless you're only planning on killing corvettes, and the other upgrades are well worth it simply because the torpedo frigate is such a good all-round unit.
Flak frigates - turn up later on in the game as they require the advanced research module, but they are brilliant at killing fighters, especially in numbers. A few of these can really protect your frigates or destroyers from fighters which they're otherwise vulnerable against. Except in very large numbers, they are not that effective against anything other than fighters, although their abillity against fighters still makes them very much worthwhile. The level1 spped/armour upgrades are good unless you're short on cash, personally I don't use these in large enough numbers to warrant lvl2 arm/speed.
Ion frigates - i've never used these much, as by the time I can build these (require an adv. res. mod) I have always upgraded my torpedo frigates, so I will tend to choose lvl2 armour for those instead of starting again with ions. However, many skilled players use them so maybe i'll play around with them some more. They are very good at killing other frigates, carriers and collectors, and in sufficient numbers will take down destroyers, although as with torpedo frigates they'll suffer bad losses so make sure you have enough to make it worthwhile. They will get cut to pieces by bombers or corvettes, so make sure you have other ship types on hand to protect them. If you're building them, their upgrades (arm/speed) are fairly useful.
Marine frigates - I use these in most games. Technically they have guns, but in reality their only use if for capturing other ships. Their are 2 basic times to use them. The first is to slip them out in the middle of a frigate battle, and try and use the odd one to take over a destroyer or carrier. Your opponent will normally notice this and put in a lot of effort to kill them, which can give you the window you need to destroy their force. The second time to use them is when you've already beaten down their force, and you have a chance to take over their carrier or ms/fs with relatively little resistance.
Destroyers - Brilliant ships. They are very durable, and pack a lot of punch against frigates, carriers and collectors. A single destroyer backing up a force or hypered into a resource patch can give your enemy real trouble. If you can get 2 or 3 into play you're normally in a very strong position. However, they really do need cover from other ship types, as bombers or corvettes can tear them apart without really suffering any losses. Many people hyperspace them in to battle to overcome their slow speed, which is a good tactic - but be careful that your opponent doesn't have a gravwell to stop this, as it will leave your destroyer damaged and out of position. Their upgrades are well worthwhile despite their cost.
Collectors - same as hiigaran, except that due to the vaygr docking you can afford to have slightly more at any given patch - drop off points are more important.
Refineries - same as hiigaran.
Probes - same as hiigaran.
Scouts - personally i don't tend to use scouts, as they come out of your fighter allowance, and i'd rather use probes and have 18 vaygr strike craft in most games. They can be good for some quick scouting, and it's far easier to keep them alive than your probes. Emp can be very effective (far more so than hiigaran emp), although personally i tend to prefer speed upgrades for the fighter class in general due to the cost of emp research and the fact that the scouts count against your fighter allowance. Note: as opposed to hw or hwc, scouts in hw2 are NOT effective combat craft. Even in large numbers, they won't kill anything larger than a probe. Their use is purely scouting/emp.
Assault Craft - fantastically useful, and essential in most games. You really need to look after your acs - if you get yourself in a position where the enemy has far more sc than you, you're normally in serious trouble. Their main use is in killing other strike craft - use them to fight your opponent's ints/acs until they have killed them, and then if you have sufficient numbers you can start to look into killing collectors, although i tend more to holding them back and keeping them alive until later in the game. Remeber that you max out at 18 assault craft, as opposed to the hiigaran 14 - the 4 extra squads can turn the tide very quickly, and you can get to lvl2 speed upgrades far faster than they can. If you can get a hiigaran opponent into an early fight then you're really well set up for the rest of the game in most situations. As a vaygr player, it's really well worth keeping your assault craft going throughout the game. Speed upgrades are critical, and I use them in every game I play as vaygr - they improve all vaygr strike craft, so they are well worthwhile, and really turn the tide of the game. Because of this, i'm assuming that you have speed upgrades for both the other classes of vaygr strike craft.
Bombers - bombers are incredibly effective, but they really need to be used at the right time. Bombers die very quickly against assault craft or interceptors, so you really need to make sure that you have at least the same number of acs/ints before you start researching/making them. Against a hiigaran opponent, one good time to use them can be once you have built 14 acs (to match his ints) and he is building frigates. Bombers should only be brought into play if the opponent has decided not to go for so many fighters, or you have already killed all or most of his ints/acs. If you do get the chance to build them they can be very effective at killing frigates (except flak/assault), picking off modules from the ms or a carrier, killing collectors, or actually killing a carrier. The 'improved bombs' upgrade is expensive, but if you know you have the chance to put it into effect it is well worth while.
Lance fighters - very useful against corvettes. Many people who play hiigaran go for corvettes against vaygr players - lance fighters will kill them fairly quickly, although they will also die themselves against gun corvettes. They are well worth slipping in against an opponent who chooses to opt for corvs, whether they're playing as hiigaran or vaygr. They can do reasonable damage to other craft as part of a large swarm that has taken down the enemy's fighters.
Missile Corvettes - these are exceptionally useful ships. They will tear apart opposing corvettes (they will even defeat pulsar corvettes), and will do reasonably well against most ship types including fighters, frigates (except torpedo frigates), collectors and destroyers. Their upgrades are well worthwhile, as they make them even tougher than they are to start with. An all-round very useful ship type, although they do not fit in to every game.
Laser Corvettes - simply devastating. Similar to bombers, they need to be used in the right situation, although they are more durable. They are simple ships - they rip through frigates (although torpedo frigates will also slaughter them in return), destroyers, carriers and collectors, but will do almost nothing against fighters or other corvettes. If you can achieve dominace in the field of fighters and corvettes, then laser vettes are best deployed against your opponent's carrier if it's exposed, as in numbers they can rip it apart in seconds. The upgrades are carried across from the missile corvette, so are well worth the cash in most situations.
Heavy missile frigates - a very effective ship class, although when i'm playing vaygr i tend to shy away from their frigates in general. Their primay use is in destroying enemy frigates and carriers, although in sufficient numbers they can also take down destroyers. They are more effective at killing frigates than upgraded torpedo frigates, so are a good counter for hem - if you can fit them into your strategy. Their upgrades are expensive, although effective, as they apply acorss the whole frigate class.
Assault frigates - I have hardly ever used this ship class, although from good sources they are effective against strike craft if used in sufficient numbers.
Infiltrator frigates - due to the fact that the cost of researching frigates in the first place is high for vaygr, imho in most cases infiltrator frigates for vaygr are so expensive as to not be truly useful.
Destroyers - although the vaygr destroyer is equal its hiigaran counterpart, in many ways it is more useful for the vaygr race. Many hiigaran counters to the vaygr depend on frigates, and if you can get this frigate-killer out it really gives your opponent another serious problem to think about. A single destroyer backing up a force or hypered into a resource patch can give your enemy real trouble. If you can get 2 or 3 into play you're normally in a very strong position. However, as with hiigaran destroyers they really do need cover from other ship types, as bombers or corvettes can tear them apart without really suffering any losses. Many people hyperspace them in to battle to overcome their slow speed, which is a good tactic - but be careful that your opponent doesn't have a gravwell to stop this, as it will leave your destroyer damaged and out of position. Check this before you invest in the hyperspace research.Upgrades for the vaygr destroyer are far more costly, as they apply across the capital ship class - but beware fighting upgraded hiigaran destroyers, as if your's are at a lower level, they will lose fairly quickly.